Re: [ccp4bb] short step

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Per-residue RMSD for multiple structures?+ CCP4BB Gestapo
From: chern chern {- at -} UALBERTA {- dot -} CA
Date: 2010-02-23

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Subject: Re: Per-residue RMSD for multiple structures? [INTERIM REPORT]
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-02-23

Subject: Re: short step
From: Ed Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2010-02-23

Ed,

thanks - this is a great suggestion. Unfortunately, it's not the
problem - I had the "oscillation start 0.0 range 0.5 step 0.001"
statement in the denzo input file. Denzo runs fine and there is no
slippage issue. I tried turning off postrefinement and both batch and
crystal rotx refinement (batch is what I do generally), to no avail.

Ed.

On Mon, 2010-02-22 at 19:11 -0500, Edward A. Berry wrote:
> Try grepping "crystal" your .x files (or whatever you called the
> denzo output files). Also grep for "start".
>
> By default denzo updates start-phi to the end
> of the previous oscillation. Since 0,5 degree is within radius of
> convergence, it re-refines crystal rotx to be compatible with this
> assumption and the oscillation photograph, which means crystal rotx
> will be moving backwards 0.5 degrees for each frame. Scalepack
> in postrefinement sees this as a serious case of "slippage" and is
> unable to postrefine a value of crystal rotx that is compatible with
> all the frames.
>
> It may be possible to turn of post-refinement with "POSTREFINE 0"
> or some such.
>
> Ed
>
> Ed Pozharski wrote:
> > I want to process bunch of frames with extremely short step - i.e. these
> > are 0.5degree oscillations but crystal only rotates by 1 degree over
> > 1000 frames (I would have kept it at the same orientation if Rigaku
> > control software would allow zero step). Denzo can process the frames
> > all right, but scalepack chokes on it saying "Floating Exception". I
> > don't have much experience with mosflm, and it failed also.
> >
> > What I wonder is if this happens because both programs have some bug in
> > these unusual conditions or there is something fundamental that prevents
> > scaling such data?
> >
> > Cheers,
> >
> > Ed.
> >

--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Per-residue RMSD for multiple structures?+ CCP4BB Gestapo
From: chern chern {- at -} UALBERTA {- dot -} CA
Date: 2010-02-23

Next message:
Subject: Re: Per-residue RMSD for multiple structures? [INTERIM REPORT]
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-02-23